Description

Fast Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ] meta is associated to the PLINK native file input

bed{:bash}

:file

PLINK binary biallelic genotype table file

*.{bed}

bim{:bash}

:file

PLINK extended MAP file

*.{bim}

fam{:bash}

:file

PLINK sample information file

*.{fam}

meta2{:bash}

:map

Groovy Map containing sample information, e.g. [ id:‘test’, single_end:false ] meta2 is associated to VCF file input

vcf{:bash}

:file

Variant calling file (vcf)

*.{vcf}

meta3{:bash}

:map

Groovy Map containing sample information, e.g. [ id:‘test’, single_end:false ] meta3 is associated to BCF file input

bcf{:bash}

:file

PLINK variant information + sample ID + genotype call binary file

*.{bcf}

meta4{:bash}

:map

Groovy Map containing sample information, e.g. [ id:‘test’, single_end:false ] meta4 is associated to phenotype file input

phe{:bash}

:file

PLINK file containing phenotype information. This phenotype information can be read from the third column with the —pheno option or from a specific column with the —pheno-name option.

*.{phe}

Output

name:type
description
pattern

fepi{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.epi.cc{:bash}

:file

PLINK fast-epistasis file

*.{epi.cc}

fepisummary{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.epi.cc.summary{:bash}

:file

PLINK fast-epistasis summary file

*.{epi.cc.summary}

flog{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.log{:bash}

:file

PLINK fast-epistasis log file

*.{log}

fnosex{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.nosex{:bash}

:file

Ambiguous sex ID file

*.{nosex}

versions_plink{:bash}

${task.process}{:bash}

:string

The name of the process

plink{:bash}

:string

The name of the tool

plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

plink{:bash}

:string

The name of the tool

plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'{:bash}

:eval

The expression to obtain the version of the tool

Tools

plink
GPL

Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

cog-genomics.org/plink cog-genomics.org/plink/1.9/data#recode https://www.cog-genomics.org/plink/1.9/dev
maintainer
Github user davidebag
get in touch
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